10-93926824-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000605679.5(SLC35G1):​n.*253+14025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,998 control chromosomes in the GnomAD database, including 18,481 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 18481 hom., cov: 32)

Consequence

SLC35G1
ENST00000605679.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.900
Variant links:
Genes affected
SLC35G1 (HGNC:26607): (solute carrier family 35 member G1) This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC35G1ENST00000605679.5 linkn.*253+14025C>G intron_variant Intron 3 of 3 1 ENSP00000474890.1 D3DR41
SLC35G1ENST00000494992.5 linkn.*253+14025C>G intron_variant Intron 3 of 4 5 ENSP00000474294.1 D3DR41

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73423
AN:
151880
Hom.:
18472
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.442
Gnomad AMI
AF:
0.462
Gnomad AMR
AF:
0.503
Gnomad ASJ
AF:
0.453
Gnomad EAS
AF:
0.945
Gnomad SAS
AF:
0.570
Gnomad FIN
AF:
0.521
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.460
Gnomad OTH
AF:
0.448
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73474
AN:
151998
Hom.:
18481
Cov.:
32
AF XY:
0.490
AC XY:
36378
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.442
Gnomad4 AMR
AF:
0.503
Gnomad4 ASJ
AF:
0.453
Gnomad4 EAS
AF:
0.946
Gnomad4 SAS
AF:
0.569
Gnomad4 FIN
AF:
0.521
Gnomad4 NFE
AF:
0.460
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.460
Hom.:
1978
Bravo
AF:
0.481
Asia WGS
AF:
0.730
AC:
2537
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
16
DANN
Benign
0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs829237; hg19: chr10-95686581; API